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mkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 11:23] – [History] mkatarimkatari-bioinformatics-august-2013-introlinuxnotes [2015/06/11 11:50] (current) – [Controlling Jobs] mkatari
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 <code> <code>
 +[2015-06-11 07:22.19]  ~
 +[Manpreet.WIN-OAOVO3NM02E] ➤ cp allusers.txt Desktop/allusers_local.txt
 +                                                                           ✔
 +────────────────────────────────────────────────────────────────────────────
 +[2015-06-11 07:22.37]  ~
 +[Manpreet.WIN-OAOVO3NM02E] ➤ scp Desktop/allusers_local.txt mkatari@hpc.ilri.cgiar.org:
 +Unauthorized access is prohibited.
 +allusers_local.txt                        100%   18KB  18.2KB/  00:00
 +
 +</code>
 +the : at the end is very important because it tells the shell that is a server and not a file name. The : by itself puts the file in your home directory, but you can specify a specific path if you wanted to.
 +
 +Now to copy the file back to my computer I will use the following command. Note that this time I am also renaming the file on my computer.
 +
 +<code>
 +[Manpreet.WIN-OAOVO3NM02E] ➤ scp mkatari@hpc.ilri.cgiar.org:allusers_local.txt ./return_allusers.txt
 +Unauthorized access is prohibited.
 +allusers_local.txt                        100%   18KB  18.2KB/  00:00
 +                 
 +</code>
 +
 +====== Controlling Jobs ======
 +
 +The following commands and keyboard short-cuts can come in handing when you need to cancel, suspend, or start a job.
 +
 +^Command^Action^
 +|ctrl-C|Terminate current running job|
 +|ctrl-Z|Suspend Jobs|
 +| bg | Once a job has been suspended ''bg'' can be put in the background |
 +| fg | In order to put a background job in the foreground type ''fg''|
 +| & | When executing a command and you want to put it in the background immediately put the ''&'' symbol at the end of the command.|
 +| jobs | This gives a list of jobs (suspended, running, and terminating)|
 +| top | This starts an interface where you can see all jobs. To see all jobs under your account type ''u'' and then when prompted, your account id.
 +
 +====== Commands for manipulating and querying files ======
 +
 +Some more cool commands
 +
 +^Command^Action^
 +|less/more | read through the file without loading the entire file. Press spacebar to continue or q to quit. |
 +|touch | create an empty file |
 +|head | show the first few lines of the file|
 +|tail | show the last few lines of the file|
 +|cat | read through the file(s)|
 +|grep | search for patterns in a file or files|
 +|cut | separate file based on columns|
 +|comm/diff | compare and see the difference between the files. The files have to be sorted before using either of these commands.|
 +|split | splits file into smaller files based on the options|
 +|sort | sort the file base on the options selected.|
 +|wc | wordcount|
 +
 +
 +
 +
 +
  
 ====== Exercise ====== ====== Exercise ======
mkatari-bioinformatics-august-2013-introlinuxnotes.1434021808.txt.gz · Last modified: 2015/06/11 11:23 by mkatari